There are more ways to affect people's trust in you....
Accidentally hurting them in battle through crossfire and explosions. Sending them into a crapshoot and getting them hurt. Telling them to charge then staying back and letting them thin out the enemies for you at their expense. Telling other team mates to heal people.
Stuff like that. And when their trust gets low enough, they will start disobeying orders and not helping you when you need it. Like when you have a giant ass robot gorilla bearing down on you and the only way your staying alive is by running away. You can only get out of that mess by asking your team mates to shoot at it and draw it's attention. If they, say....disobey you, well, your right fucked.
So I wouldn't say it's completely superficial. It punishes players who are careless and use their squad as a means to an end rather then treating them as people. It helps feed into a story that is about comradery and team work, and helps you actually care about the characters. So I wouldn't say it's completely superficial. Though more probably could have been done with it. I don't believe you can get alternate cutscenes in accordance to your team mate's trust level, right?